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. 2016 Apr 19:17:172.
doi: 10.1186/s12859-016-1016-7.

Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves

Kathleen Sprouffske  1   2 , Andreas Wagner  3   4   5
Affiliations

Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves

Kathleen Sprouffske et al. BMC Bioinformatics. .

Abstract

Background: Plate readers can measure the growth curves of many microbial strains in a high-throughput fashion. The hundreds of absorbance readings collected simultaneously for hundreds of samples create technical hurdles for data analysis.

Results: Growthcurver summarizes the growth characteristics of microbial growth curve experiments conducted in a plate reader. The data are fitted to a standard form of the logistic equation, and the parameters have clear interpretations on population-level characteristics, like doubling time, carrying capacity, and growth rate.

Conclusions: Growthcurver is an easy-to-use R package available for installation from the Comprehensive R Archive Network (CRAN). The source code is available under the GNU General Public License and can be obtained from Github (Sprouffske K, Growthcurver sourcecode, 2016).

Keywords: Experimental evolution; Growth curve; Logistic.

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Figures

Fig. 1
Fig. 1
Comparisons of Growthcurver’s growth curve metrics for experimental data from 937 replicate E. coli populations. We plotted the growth curve metrics in a pairwise fashion to identify correlations between metrics. The metrics are listed in the diagonal (growth rate, doubling time, the logarithm of the initial population size, the area under the logistic curve, the area under the experimentally-measured curve, and the carrying capacity). We plotted the pairwise comparisons in the lower diagonal; for example, in the panel comparing growth rate and doubling time, each point is the growth rate and doubling time obtained from Growthcurver for a single experimental replicate. The Spearman correlation of any panel in the lower diagonal is reported in the upper diagonal
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